Noninvasive population assessment of moose (Alces alces) by SNP genotyping of fecal pellets

Ida-Maria Blåhed,Göran Spong,Göran Ericsson

doi:10.1007/s10344-019-1337-8

Abstract

Noninvasive genetic studies of wild animals enable the recovery of information infeasible to obtain using other means. However, the low quantity and quality of noninvasively collected DNA often challenge the retrieval of reliable genotypes, which may cause biases in downstream analyses. In this study, we optimized SNP (single nucleotide polymorphism) genotyping of fecal samples from moose (Alces alces) with the main purpose of exploring the potential of using noninvasively retrieved genotypes for individual- and sex identification. Fecal pellets were collected during the late winter of 2016 on the Swedish island of Öland in the Baltic Sea and DNA was extracted and genotyped using 86 autosomal, six sex-specific and five species diagnostic SNPs. The SNP error rate of the quality filtered dataset was 0.06 and the probability of identity for siblings below 0.001. Following a thorough quality filtering process, 182 reliable genotypes were obtained, corresponding to 100 unique individuals (37 males, 63 females), with an estimated male proportion of 37% (± 9%). The population size, estimated using two different capture-mark-recapture approaches, was found to be in the range of 115–156 individuals (95% CI). Furthermore, moose on Öland showed significantly lower heterozygosity levels (zHexp = −5.51, N = 69, pHexp = 3.56·10−8, zHobs = −3.58, N = 69, pHobs = 3.38·10−4) and appeared genetically differentiated from moose on the Swedish mainland. Thus, we show that quality controlled noninvasively derived SNP genotypes can be highly informative for individual and population monitoring in a large ungulate.

Highlights

Acquiring reliable data on fundamental parameters such as distribution, population size, and reproduction is important for wildlife research and management alike (Allendorf and Hard 2009; Bender 2006; DeYoung et al 2006; Morellet et al 2007)
We evaluate the population monitoring capacity of single nuclear polymorphism (SNP) genotyping of noninvasively collected fecal pellets of moose
For each encountered “pile” of moose fecal pellets, five pellets were collected into a plastic bag, and the samples were stored in freezer until DNA extraction

Summary

Introduction

Acquiring reliable data on fundamental parameters such as distribution, population size, and reproduction is important for wildlife research and management alike (Allendorf and Hard 2009; Bender 2006; DeYoung et al 2006; Morellet et al 2007). Many different observational methods have been used to generate such estimates, ranging from spoor and pellet counts to camera-trapping, ringing, collaring, and aerial surveys. These methods may produce good relative population estimates, allowing for comparisons between censuses and monitoring of population trends over time (Balme et al 2009; Cutler and Swann 1999); converting observation frequencies to absolute numbers is typically fraught with biases (Anderson 2001; Anderson 2003; Garel et al 2010; Lonergan et al 2013; Ringvall et al 2000). An alternative is to use an individual’s genotype; a unique and permanent tag that can be obtained noninvasively, i.e., from remnants such as feces, 96 Page 2 of 11

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